During a battle, a lone Dalek was damaged by weapon fire which penetrated its casing, allowing for a parasitic wasp to enter the body. Once the Dalek returned to base, it was deemed damaged and sent to the repair bay where its genetic material was to be analysed. This was part of the Daleks' standard practice of taking the DNA to the reproductive factories for the breeding of more Daleks. It was at this point that the Dalek Emperor from an alternate future arrived and informed them of a great catastrophe that would befall them and provided them a cure; an insecticide that would prevent a so-called "Mutant Phase" from occurring.

The Daleks distributed this cure amongst themselves and continued in their conquests. However, the pesticide cure did not work on this early stage of the mutation and the genetic elements of the wasp began to spread throughout the Dalek population. Thus began a period of deadly transformations where Daleks broke free from their casings as the Mutant Phase began to attack everything in its path. Skaro itself was assaulted and the Dalek Empire was besieged by the countless hordes of the Mutant Phase.

The creatures began to spread across the universe and devastated the planetEarth. However, they mysteriously died on the planet due to the ingestion of a pesticide that affected them. This resulted in the Daleks using the technical knowledge of Professor Ptolem to provide a cure and when the Fifth Doctor arrived, the Dalek Emperor planned to use him to prevent the infection from starting in the first place by travelling back in time to the source of the Mutant Phase. Taking the pesticide cure, the Dalek Emperor, in a mind-wiped host body, approached the Daleks and informed them of the catastrophe. It was at this point that the Doctor and itself became aware that the source of the Mutant Phase was the Emperor's attempt at stopping them. Had he not interfered then the Daleks would have removed the alien genetic material and the Mutant Phase would never have developed.

Learning the truth, this alternate reality version of the Dalek Emperor destroyed the cure, thus erasing himself and the Mutant Phase from existence.

The creation of the Mutant Phase was ultimately a paradox that was centred not around the Mutant Phase but the Dalek Emperor who inadvertently aided in its creation. However, by breaking the cycle, the Emperor prevented its formation in the first place and as such the Mutant Phase did not exist in the mainstream universe. (AUDIO: The Mutant Phase)

The mutation affected the Dalek mutant itself. The mutation started with a gestation period indicated by disorientation, after which the Dalek mutant broke through its own battle armour and began to grow at an accelerated rate. Its ultimate form was that of a large insectoid creature with metallic wings. These creatures were capable of absorbing energy and laying waste to entire planets in large swarms.

During the transformation, the higher brain functions of the Dalek are lost and the resulting creature works through primal instincts only. This meant that they were a swarm of mindless destructive beasts that consumed whole civilisations and laid waste to the universe. While the Daleks were described as evil incarnate, the Mutant Phase was deemed as a threat that was far more dangerous. (AUDIO: The Mutant Phase)